Question

Derive weights for sequences

ACTA

ACTT

CGTT

AGAT

using Thompson, Higgins, and Gibson method

Use the outline below (a-d) to solve this problem

a) compute pairwise distances between sequences

b) apply UPGMAmethod to join sequences and consequently the clusters)

c) build a phylogenetic tree

d) derive sequence weights

Answer 1

ACTA => Seq p

ACTT => Seq q

CGTT => Seq r

AGAT => Seq s

a) Distance between i and j is denoted by d_i,j = Number of mismatch / Total number of nucleotides

d_p,q = 1/4 = 0.25

d_p,r = 3/4 = 0.75

d_p,s = 3/4 = 0.75

d_q,r = 2/4 = 0.5

d_q,s = 2/4 = 0.5

d_r,s = 2/4 = 0.5

b) Distance matrix

For easy computing, multiplying all the table values by 4.

c) Least distance = 1 (between p and q)

So p and q forms a clade.

Depth of branch = Least distance/ 2 = 1/2 =0.5

Distance between pq and r = (distance betrween p and r + distance between q and r)/2 = (3+2)/2 = 2.5

Distance between pq and s = (distance betrween p and s+distance between q and s)/2 = (3+2)/2 = 2.5

New matrix is as below

Doing the steps to obtain phylogeny.

(sequence weights are indicated in red color)